From: Ilya Chorny (ichorny_at_gmail.com)
Date: Tue Jun 05 2007 - 10:45:33 CDT
Hello All,
I am getting a Rattle error approximately 1 ns into my simulation. I restart
the simulation and it runs fine for about 300ps - 1ns and then gives me the
rattle error. All the other posts seem to get the rattle error early on in
the simulation. My simulation Info output as well as the first time step are
below. Thanks in advance.
Cheers,
Ilya
Info: NAMD 2.6 for Linux-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux-iccstatic
Info: Built Wed Aug 30 12:54:30 CDT 2006 by jim on kyoto.ks.uiuc.edu
Info: 1 NAMD 2.6 Linux-i686 16 compute-0-0.local chorny
Info: Running on 16 processors.
Info: 7376 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Changed directory to .
Info: Configuration file is NeRh50_run.conf
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE NeRh50_run3.restart.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 113 0 0
Info: PERIODIC CELL BASIS 2 0 113 0
Info: PERIODIC CELL BASIS 3 0 0 77.864
Info: PERIODIC CELL CENTER 7.2 8.3 -0.78
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 310
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME Ne50_run4.dcd
Info: DCD FREQUENCY 500
Info: DCD FIRST STEP 500
Info: DCD FREQUENCY 500
Info: DCD FIRST STEP 500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME NeRh50_run4.xst
Info: XST FREQUENCY 500
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME NeRh50_run4
Info: RESTART FILENAME NeRh50_run4.restart
Info: RESTART FREQUENCY 500
Info: BINARY RESTART FILES WILL BE USED
Info: CUTOFF 12
Info: PAIRLIST DISTANCE 13.5
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0.96
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16.96
Info: ENERGY OUTPUT STEPS 500
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 5000
Info: PRESSURE OUTPUT STEPS 500
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 200 FS
Info: DECAY TIME IS 100 FS
Info: PISTON TEMPERATURE IS 310 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS -0.000137713 -0.000132993 8.54564e-06
Info: CELL FLUCTUATION IS ANISOTROPIC
Info: CONSTANT AREA PRESSURE CONTROL ACTIVE
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 128 128 128
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-i686.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-i686.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1181056615
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ./NeRh50_run1.coor
Info: STRUCTURE FILE ./NeRh_equilibrated_no_TIPC.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS
/home/chorny/namd/c31b1/par_all27_prot_lipid.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES ./NeRh50_run3.restart.coor
Info: SUMMARY OF PARAMETERS:
Info: 180 BONDS
Info: 447 ANGLES
Info: 566 DIHEDRAL
Info: 46 IMPROPER
Info: 6 CROSSTERM
Info: 114 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 101489 ATOMS
Info: 80856 BONDS
Info: 94985 ANGLES
Info: 104954 DIHEDRALS
Info: 2942 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 84334 RIGID BONDS
Info: 220133 DEGREES OF FREEDOM
Info: 37757 HYDROGEN GROUPS
Info: TOTAL MASS = 618752 amu
Info: TOTAL CHARGE = 4.07752e-05 e
Info: *****************************
Info: Entering startup phase 0 with 39252 kB of memory in use.
Info: Entering startup phase 1 with 39252 kB of memory in use.
Info: Entering startup phase 2 with 57784 kB of memory in use.
Info: Entering startup phase 3 with 58580 kB of memory in use.
Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 4 (PERIODIC)
Info: REMOVING COM VELOCITY -0.0187958 0.0141929 0.0178001
Info: LARGEST PATCH (45) HAS 785 ATOMS
Info: CREATING 12797 COMPUTE OBJECTS
Info: Entering startup phase 4 with 75108 kB of memory in use.
Info: PME using 16 and 16 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Entering startup phase 5 with 75632 kB of memory in use.
Info: Entering startup phase 6 with 75632 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 75632 kB of memory in use.
Info: CREATING 12797 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.3715e-16 AT 0.03125
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.00929e-16 AT 0.231756
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 3.70577e-22 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.80873e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 7.88861e-30 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.02552e-29 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 8.43724e-23 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 9.51258e-23 AT 11.9974
Info: Entering startup phase 8 with 76584 kB of memory in use.
Info: Finished startup with 76584 kB of memory in use.
TCL: Running for 1000000 steps
PRESSURE: 0 -78.6193 6.80917 89.9077 6.80917 23.4063 67.2699 89.9077 67.2699-
14.332
GPRESSURE: 0 -62.8527 154.268 51.7709 133.495 59.2651 81.6383 13.3791 -
1.4299 -3.49497
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 5873.2545 23500.7596 10897.2134
634.0980
-256491.1768 6072.8216 0.0000 0.0000 67690.5902
-141822.4395 309.4807 -141379.3407 -141379.3407
309.4807
-23.1817 -2.3609 994245.4160 -23.1817 -2.3609
-- Ilya Chorny Ph.D.
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